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United States Department of Agriculture

Agricultural Research Service

Title: Comparative Analyses of Potato Expressed Sequence Tag Libraries

Authors
item Ronning, Catherine - TIGR ROCKVILLE MD
item Stegalkina, Svetlana - TIGR ROCKVILLE MD
item Ascenzi, Robert - TIGR ROCKVILLE MD
item Bougri, Oleg - TIGR ROCKVILLE MD
item Hart, Amy - TIGR ROCKVILLE MD
item Utterbach, Teresa - TIGR ROCKVILLE MD
item Vanaken, Susan - TIGR ROCKVILLE MD
item Riedmuller, Steve - TIGR ROCKVILLE MD
item White, Joseph - TIGR ROCKVILLE MD
item Cho, Jennifer - TIGR ROCKVILLE MD
item Pertea, Geo - TIGR ROCKVILLE MD
item Lee, Yuandan - TIGR ROCKVILLE MD
item Karamycheva, Svetlana - TIGR ROCKVILLE MD
item Sultana, Razvan - TIGR ROCKVILLE MD
item Tsai, Jennifer - TIGR ROCKVILLE MD
item Quackenbush, John - TIGR ROCKVILLE MD
item Griffiths, Helen - TIGR ROCKVILLE MD
item Restrepo, Silvia - CORNELL UNIV ITHACA NY
item Smart, Christine - CORNELL UNIV ITHACA NY
item Fry, William - CORNELL UNIV ITHACA NY
item Van Der Hoeven, Rutger - CORNELL UNIV ITHACA NY
item Tanksley, Steve - CORNELL UNIV ITHACA NY
item Zhang, Peifen - ARS-UCB PLNT GENE EXP CTR
item Jin, Hailing - ARS-UCB PLNT GENE EXP CTR
item Yamamoto, Miki - ARS-UCB PLNT GENE EXP CTR
item Baker, Barbara
item Buell, C. Robin - TIGR ROCKVILLE MD

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 23, 2003
Publication Date: February 1, 2003
Citation: RONNING, C.M., STEGALKINA, S.S., ASCENZI, R.A., BOUGRI, O., HART, A.L., UTTERBACH, T.R., VANAKEN, S.E., RIEDMULLER, S.B., WHITE, J.A., CHO, J., PERTEA, G.M., LEE, Y., KARAMYCHEVA, S., SULTANA, R., TSAI, J., QUACKENBUSH, J., GRIFFITHS, H.M., RESTREPO, S., SMART, C.D., FRY, W.E., VAN DER HOEVEN, R., TANKSLEY, S., ZHANG, P., JIN, H., YAMAMOTO, M.L., BAKER, B.J., BUELL, C. COMPARATIVE ANALYSES OF POTATO EXPRESSED SEQUENCE TAG LIBRARIES. PLANT PHYSIOLOGY. 2003. 131:419-429.

Interpretive Summary: The cultivated potato (Solanum tuberosum) shares similar biology with other members of the Solanaceae, yet has features unique within the family, such as modified stems (stolons) that develop into edible tubers. To better understand potato biology, we have undertaken a survey of the potato transcriptome using expressed sequence tags (ESTs) from diverse tissues. Using hierarchal and k means clustering of the EST sequences, we were able to correlate changes in gene expression with major physiological events in potato biology. Using pair-wise comparisons of tuber-related tissues, we were able to associate genes with tuber initiation, dormancy, and sprouting. We also were able to identify a number of characterized as well as novel sequences that were unique to the incompatible interaction of late-blight pathogen, thereby providing a foundation for further understanding the mechanism of resistance.

Technical Abstract: The cultivated potato (Solanum tuberosum) shares similar biology with other members of the Solanaceae, yet has features unique within the family, such as modified stems (stolons) that develop into edible tubers. To better understand potato biology, we have undertaken a survey of the potato transcriptome using expressed sequence tags (ESTs) from diverse tissues. A total of 61,940 ESTs were generated from aerial tissues, below-ground tissues, and tissues challenged with the late-blight pathogen (Phytophthora infestans). Clustering and assembly of these ESTs resulted in a total of 19,892 unique sequences with 8,741 tentative consensus sequences and 11,151 singleton ESTs. We were able to identify a putative function for 43.7% of these sequences. A number of sequences (48) were expressed throughout the libraries sampled, representing constitutively expressed sequences. Other sequences (13,068, 21%) were uniquely expressed and were detected only in a single library. Using hierarchal and k means clustering of the EST sequences, we were able to correlate changes in gene expression with major physiological events in potato biology. Using pair-wise comparisons of tuber-related tissues, we were able to associate genes with tuber initiation, dormancy, and sprouting. We also were able to identify a number of characterized as well as novel sequences that were unique to the incompatible interaction of late-blight pathogen, thereby providing a foundation for further understanding the mechanism of resistance.

Last Modified: 9/23/2014
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